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Basic information

Entry
Database: PDB / ID: 4we7
TitleStructure and receptor binding preferences of recombinant human A(H3N2) virus hemagglutinins
ComponentsHemagglutinin HA1 chain
KeywordsVIRAL PROTEIN / Hemagglutinin / HA1 / H3N2 / influenza virus
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsYang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Villanueva, J.M. / Stevens, J.
CitationJournal: Virology / Year: 2015
Title: Structure and receptor binding preferences of recombinant human A(H3N2) virus hemagglutinins.
Authors: Yang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Villanueva, J.M. / Stevens, J.
History
DepositionSep 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / diffrn_detector ...citation / diffrn_detector / entity / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA1 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,40318
Polymers126,3064
Non-polymers3,09714
Water2,144119
1
A: Hemagglutinin HA1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4615
Polymers31,5761
Non-polymers8854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemagglutinin HA1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2404
Polymers31,5761
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hemagglutinin HA1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4615
Polymers31,5761
Non-polymers8854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hemagglutinin HA1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2404
Polymers31,5761
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.298, 214.898, 101.807
Angle α, β, γ (deg.)90.00, 103.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hemagglutinin HA1 chain


Mass: 31576.496 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Alberta/026/2012(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: U3N7S5
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.07 Å3/Da / Density % sol: 69.75 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6 / Details: 0.2M Calcium acetate, 0.1M MES, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 67875 / % possible obs: 98.1 % / Redundancy: 3.4 % / Net I/σ(I): 8.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementResolution: 2.5→42.98 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2511 3431 5.05 %
Rwork0.2184 --
obs0.2202 67875 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→42.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8512 0 196 119 8827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098946
X-RAY DIFFRACTIONf_angle_d1.26412142
X-RAY DIFFRACTIONf_dihedral_angle_d15.7593324
X-RAY DIFFRACTIONf_chiral_restr0.081336
X-RAY DIFFRACTIONf_plane_restr0.0071574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.53430.41251140.35541901X-RAY DIFFRACTION72
2.5343-2.57050.41091280.31422523X-RAY DIFFRACTION96
2.5705-2.60880.36771350.31032528X-RAY DIFFRACTION96
2.6088-2.64960.30641330.30052490X-RAY DIFFRACTION95
2.6496-2.6930.32961250.30262633X-RAY DIFFRACTION98
2.693-2.73940.33371170.2912579X-RAY DIFFRACTION99
2.7394-2.78930.36581310.29042607X-RAY DIFFRACTION99
2.7893-2.84290.37961290.29672703X-RAY DIFFRACTION100
2.8429-2.90090.36041560.29492554X-RAY DIFFRACTION100
2.9009-2.9640.35831390.27962609X-RAY DIFFRACTION100
2.964-3.03290.3341520.2752633X-RAY DIFFRACTION100
3.0329-3.10870.32391430.262629X-RAY DIFFRACTION100
3.1087-3.19280.31991410.26972668X-RAY DIFFRACTION100
3.1928-3.28670.28321230.25782626X-RAY DIFFRACTION100
3.2867-3.39270.34971230.26882659X-RAY DIFFRACTION100
3.3927-3.51390.32691290.26532633X-RAY DIFFRACTION99
3.5139-3.65450.29561550.2392583X-RAY DIFFRACTION99
3.6545-3.82080.26861330.22962601X-RAY DIFFRACTION99
3.8208-4.02210.25441560.20612613X-RAY DIFFRACTION98
4.0221-4.27380.20041670.18892564X-RAY DIFFRACTION99
4.2738-4.60350.20461330.16792610X-RAY DIFFRACTION99
4.6035-5.06610.17931410.1632599X-RAY DIFFRACTION99
5.0661-5.79770.20561330.17292645X-RAY DIFFRACTION99
5.7977-7.29860.21751480.19942646X-RAY DIFFRACTION100
7.2986-42.98620.19641470.19442608X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0004-0.00060.00020.00310.00180.0040.0034-0.0206-0.01180.0450.01630.0524-0.0046-0.01460.00010.8063-0.46490.04180.6990.02670.5561-12.458294.388692.8691
20.00170.00210.00780.0413-0.00220.02320.018-0.0429-0.0050.0495-0.03790.00150.0229-0.0117-0.05430.6116-0.4817-0.03140.45930.02550.28921.401107.987977.3915
30.00990.00690.01560.02230.00790.04040.0816-0.083-0.07660.0912-0.082-0.00930.1686-0.0831-0.08890.277-0.4604-0.06170.0030.02870.125911.1742108.029362.1391
40.0011-0.0014-0.0020.00060.00190.00210.009-0.00170.01820.0080.01570.0215-0.0215-0.016500.5247-0.0940.08350.56860.02190.5272-0.9101122.276861.6565
50.0030.00670.00380.01520.00880.00750.01330.0157-0.0579-0.04550.0167-0.02080.0291-0.006-0.00350.4552-0.14740.07970.1507-0.05450.32767.3748100.124459.6931
60.0149-0.0098-0.04460.0130.02590.09970.024-0.116-0.07540.1361-0.1240.08560.1038-0.1279-0.08880.6236-0.45480.07750.3860.00480.3415-4.923197.186481.6265
70.00740.00380.00370.00190.00170.00190.0217-0.00380.01550.01130.0131-0.0292-0.00960.0006-0.00040.6379-0.35090.02180.5647-0.02990.563-16.472690.156283.902
80.03130.03510.02810.07680.09820.156-0.01060.02390.0851-0.03430.0701-0.0324-0.10410.04920.00940.06570.00610.01410.16240.0140.125130.8226149.191513.3762
90.0161-0.01510.0040.0151-0.00620.02480.0020.00660.00610.01030.0209-0.0307-0.00450.02130.03280.0950.0743-0.00530.28440.02450.263326.7132139.197621.6235
100.0288-0.03070.04390.0676-0.05050.11580.03970.12210.0134-0.03480.03160.11260.0166-0.15820.10510.01080.0534-0.04950.1852-0.01520.148513.7216133.841533.0909
110.01830.0269-0.01940.0448-0.03230.022-0.0107-0.025-0.00460.0032-0.0566-0.0365-0.00650.0558-0.0420.3131-0.1057-0.07450.2441-0.05460.325921.9663125.315632.3554
120.00720.005200.00450.00160.0112-0.01790.0228-0.0229-0.00860.00340.03440.0387-0.0455-0.00560.1019-0.0423-0.04830.1887-0.03590.131115.6571127.90521.6511
130.00580.0018-0.00460.0022-0.00190.00720.00570.04180.0001-0.00960.00450.00060.002-0.01360.00860.0499-0.0049-0.01640.17170.00870.056918.6873137.166418.7813
140.02070.01750.00360.02170.00540.020.02520.02110.0237-0.01530.017-0.0002-0.01730.01970.02930.0978-0.08010.03380.2262-0.00220.060339.6355151.13383.2299
150.0019-0.0018-0.00060.000900.003-0.00490.0167-0.01120.0042-0.0038-0.0060.00130.0051-0.00010.35470.01350.01460.37950.00880.200539.718142.28990.8995
160.0001-0.0001-0.0002-0.00040.00120.00170.0170.02830.0186-0.04620.03130.0860.0092-0.02650.00040.89720.4613-0.03390.8312-0.04090.6088-12.5538181.48786.1348
170.0001-0.00520.00190.0014-0.0030.00710.01720.0433-0.0167-0.0409-0.02710.0188-0.0136-0.01810.00130.56850.48890.00620.4058-0.00330.27051.3088167.902321.5319
180.0132-0.0159-0.00050.0198-0.01590.01880.09350.08710.0234-0.0859-0.0588-0.0181-0.0761-0.02330.0760.33730.37450.04090.08220.03340.214311.7863166.984634.8647
19-0.0004-0.00110.00110.00680.0002-0.00030.0065-0.03720.040.0216-0.0209-0.0004-0.0142-0.0083-00.42870.17010.06110.2317-0.00390.29937.131172.759247.1275
200.0162-0.0031-0.01090.00480.00170.01310.06540.0019-0.00090.03210.03820.01120.002-0.05020.00130.63470.1904-0.11190.3412-0.04150.49953.9662166.297238.5694
210.01690.01290.04760.01510.02120.09980.03450.11640.0306-0.1408-0.12190.1015-0.0845-0.1131-0.08570.58880.459-0.01290.39130.01440.3083-5.0014178.74417.4116
220.00010-0.00050.0002-0.00040.0010.01230-0.0139-0.0122-0.0013-0.00310.0227-0.0118-00.56780.3132-0.01010.5495-0.01720.4733-16.8018185.575915.0985
230.0032-0.0154-0.01880.11050.13720.16870.0295-0.0324-0.1080.0640.0689-0.0530.14720.03290.00330.1534-0.0496-0.03550.2730.03190.202531.0108126.578785.5805
240.03870.03380.01140.02860.00630.04150.01750.0032-0.03110.00110.0073-0.06680.01220.06110.04270.0563-0.080.00160.24570.01570.205226.8383136.568377.3462
250.07880.02330.07750.0665-0.03530.14260.0265-0.0906-0.00160.00910.00760.0454-0.0058-0.13090.1199-0.0025-0.02190.00340.1194-0.02340.111213.8376141.918965.889
260.0054-0.0075-0.00340.00740.0040.00210.00810.00190.0056-0.0132-0.0018-0.0138-0.0225-0.00550.00020.24650.03330.05750.1725-0.05970.204115.361154.700572.5895
270.0024-0.0024-0.00090.0021-0.00040.0010.00130.01090.0013-0.0155-0.0012-0.0250.00790.021800.32060.10140.0260.36520.06770.398630.7867144.597959.0921
280.0115-0.0129-0.02440.01420.02520.0561-0.0225-0.05370.01110.0193-0.02410.0336-0.0313-0.0348-0.02110.13970.0510.03410.264-0.020.14715.8672147.873677.3398
290.0441-0.0346-0.02250.11920.03240.0172-0.0232-0.09450.01330.05870.0554-0.06520.03610.05160.04240.02420.0274-0.01180.23180.02140.091630.7678130.878688.766
300.0001-00.0005-0.0002-0.00010.00060.0043-0.0113-0.0003-0.00060.0155-0.0003-0.01050.004200.1349-0.0156-0.01080.28370.06160.140240.128133.374498.0961
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 174 )
4X-RAY DIFFRACTION4chain 'A' and (resid 175 through 188 )
5X-RAY DIFFRACTION5chain 'A' and (resid 189 through 207 )
6X-RAY DIFFRACTION6chain 'A' and (resid 208 through 258 )
7X-RAY DIFFRACTION7chain 'A' and (resid 259 through 270 )
8X-RAY DIFFRACTION8chain 'B' and (resid -1 through 49 )
9X-RAY DIFFRACTION9chain 'B' and (resid 50 through 82 )
10X-RAY DIFFRACTION10chain 'B' and (resid 83 through 155 )
11X-RAY DIFFRACTION11chain 'B' and (resid 156 through 188 )
12X-RAY DIFFRACTION12chain 'B' and (resid 189 through 207 )
13X-RAY DIFFRACTION13chain 'B' and (resid 208 through 229 )
14X-RAY DIFFRACTION14chain 'B' and (resid 230 through 258 )
15X-RAY DIFFRACTION15chain 'B' and (resid 259 through 270 )
16X-RAY DIFFRACTION16chain 'C' and (resid -1 through 20 )
17X-RAY DIFFRACTION17chain 'C' and (resid 21 through 64 )
18X-RAY DIFFRACTION18chain 'C' and (resid 65 through 155 )
19X-RAY DIFFRACTION19chain 'C' and (resid 156 through 174 )
20X-RAY DIFFRACTION20chain 'C' and (resid 175 through 207 )
21X-RAY DIFFRACTION21chain 'C' and (resid 208 through 258 )
22X-RAY DIFFRACTION22chain 'C' and (resid 259 through 270 )
23X-RAY DIFFRACTION23chain 'D' and (resid -1 through 49 )
24X-RAY DIFFRACTION24chain 'D' and (resid 50 through 82 )
25X-RAY DIFFRACTION25chain 'D' and (resid 83 through 155 )
26X-RAY DIFFRACTION26chain 'D' and (resid 156 through 174 )
27X-RAY DIFFRACTION27chain 'D' and (resid 175 through 188 )
28X-RAY DIFFRACTION28chain 'D' and (resid 189 through 207 )
29X-RAY DIFFRACTION29chain 'D' and (resid 208 through 258 )
30X-RAY DIFFRACTION30chain 'D' and (resid 259 through 270 )

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